data_6T0V # _model_server_result.job_id k0XdwPsCwyZAfMnbwh2_Ow _model_server_result.datetime_utc '2024-10-20 12:45:14' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 6t0v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":801}' # _entry.id 6T0V # _exptl.entry_id 6T0V _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 483.156 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 6T0V _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6T0V _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 9 _struct_asym.id J _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 F O3E GTG 1 M GTG 1 1_555 F P A 2 M A 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.598 ? metalc ? metalc1 A OE1 GLU 94 A GLU 80 1_555 I MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc2 A OD2 ASP 122 A ASP 108 1_555 H MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.884 ? metalc ? metalc3 A OD1 ASP 122 A ASP 108 1_555 I MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.871 ? metalc ? metalc4 A OE2 GLU 133 A GLU 119 1_555 H MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.873 ? metalc ? metalc5 A O ILE 134 A ILE 120 1_555 H MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.885 ? metalc ? metalc6 G O11 M4H . A M4H 801 1_555 H MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.859 ? metalc ? metalc7 G O10 M4H . A M4H 801 1_555 I MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.913 ? metalc ? metalc8 B O GLY 313 B GLY 304 1_555 L MG MG . B MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.777 ? metalc ? metalc9 B OD2 ASP 314 B ASP 305 1_555 K MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.825 ? metalc ? metalc10 B OD1 ASP 314 B ASP 305 1_555 M MG MG . B MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc11 B O ASN 315 B ASN 306 1_555 K MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc12 B OD2 ASP 454 B ASP 445 1_555 K MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.799 ? metalc ? metalc13 B OD1 ASP 454 B ASP 445 1_555 M MG MG . B MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc14 B OD2 ASP 455 B ASP 446 1_555 M MG MG . B MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? metalc ? metalc15 J O2A 2KH . B 2KH 801 1_555 K MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc16 J O1B 2KH . B 2KH 801 1_555 K MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc17 J O2G 2KH . B 2KH 801 1_555 K MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc18 M MG MG . B MG 804 1_555 F O3' G 26 M G 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? hydrog WATSON-CRICK hydrog1 E N3 C 5 R C 18 1_555 F N1 G 26 M G 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 E N4 C 5 R C 18 1_555 F O6 G 26 M G 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 E O2 C 5 R C 18 1_555 F N2 G 26 M G 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 E N3 C 6 R C 19 1_555 F N1 G 25 M G 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 E N4 C 6 R C 19 1_555 F O6 G 25 M G 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 E O2 C 6 R C 19 1_555 F N2 G 25 M G 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 E N3 U 7 R U 20 1_555 F N1 A 24 M A 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 E O4 U 7 R U 20 1_555 F N6 A 24 M A 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 E N3 C 8 R C 21 1_555 F N1 G 23 M G 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 E N4 C 8 R C 21 1_555 F O6 G 23 M G 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 E O2 C 8 R C 21 1_555 F N2 G 23 M G 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 E N3 U 9 R U 22 1_555 F N1 A 22 M A 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 E O4 U 9 R U 22 1_555 F N6 A 22 M A 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 E N1 G 10 R G 23 1_555 F N3 C 21 M C 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 E N2 G 10 R G 23 1_555 F O2 C 21 M C 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 E O6 G 10 R G 23 1_555 F N4 C 21 M C 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 E N3 C 11 R C 24 1_555 F N1 G 20 M G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 E N4 C 11 R C 24 1_555 F O6 G 20 M G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 E O2 C 11 R C 24 1_555 F N2 G 20 M G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 E N3 U 12 R U 25 1_555 F N1 A 19 M A 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 E O4 U 12 R U 25 1_555 F N6 A 19 M A 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-C MISPAIR' hydrog22 E O2 U 12 R U 25 1_555 E N4 C 14 R C 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 E N3 U 13 R U 26 1_555 F N1 A 18 M A 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 E O4 U 13 R U 26 1_555 F N6 A 18 M A 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-A MISPAIR' hydrog25 D N6 A 1 V A 1 1_555 D N3 A 10 V A 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 D N1 G 2 V G 2 1_555 D N3 C 9 V C 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 D N2 G 2 V G 2 1_555 D O2 C 9 V C 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 D O6 G 2 V G 2 1_555 D N4 C 9 V C 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 D N3 U 3 V U 3 1_555 D N1 A 8 V A 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 D O4 U 3 V U 3 1_555 D N6 A 8 V A 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-A MISPAIR' hydrog31 D N3 A 4 V A 4 1_555 D N6 A 7 V A 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H16 N3 O14 P3' _chem_comp.formula_weight 483.156 _chem_comp.id 2KH _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag O2' C2' 2KH sing 1 n n O3' C3' 2KH sing 2 n n C2' C3' 2KH sing 3 n n C2' C1' 2KH sing 4 n n O2 C2 2KH doub 5 n n C3' C4' 2KH sing 6 n n C1' N1 2KH sing 7 n n C1' O4' 2KH sing 8 n n C2 N1 2KH sing 9 n n C2 N3 2KH sing 10 n n C4' O4' 2KH sing 11 n n C4' C5' 2KH sing 12 n n N1 C6 2KH sing 13 n n N3 C4 2KH sing 14 n n C5' O5' 2KH sing 15 n n C6 C5 2KH doub 16 n n C4 C5 2KH sing 17 n n C4 O4 2KH doub 18 n n O2B PB 2KH doub 19 n n O5' PA 2KH sing 20 n n N3A PB 2KH sing 21 n n N3A PA 2KH sing 22 n n PB O1B 2KH sing 23 n n PB O3B 2KH sing 24 n n PA O1A 2KH doub 25 n n PA O2A 2KH sing 26 n n O3B PG 2KH sing 27 n n PG O2G 2KH doub 28 n n PG O1G 2KH sing 29 n n PG O3G 2KH sing 30 n n O2A H1 2KH sing 31 n n N3A H2 2KH sing 32 n n O1B H3 2KH sing 33 n n O1G H4 2KH sing 34 n n O3G H5 2KH sing 35 n n C5' H6 2KH sing 36 n n C5' H7 2KH sing 37 n n C4' H8 2KH sing 38 n n C1' H9 2KH sing 39 n n C2' H10 2KH sing 40 n n O2' H11 2KH sing 41 n n C3' H12 2KH sing 42 n n O3' H13 2KH sing 43 n n C6 H14 2KH sing 44 n n N3 H15 2KH sing 45 n n C5 H16 2KH sing 46 n n # _atom_sites.entry_id 6T0V _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code G 7 M4H A 1 801 1 M4H 483 . H 8 MG A 1 802 901 MG MG . I 8 MG A 1 803 902 MG MG . J 9 2KH B 1 801 1 2KH 2KH . K 8 MG B 1 802 1 MG MG . L 8 MG B 1 803 2 MG MG . M 8 MG B 1 804 3 MG MG . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PA 2KH . . . J 9 127.154 136.912 147.566 1 26.77 ? PA 2KH 801 B 1 HETATM 2 O O1A 2KH . . . J 9 127.723 135.528 147.305 1 26.77 ? O1A 2KH 801 B 1 HETATM 3 O O2A 2KH . . . J 9 128.19 137.746 148.181 1 26.77 ? O2A 2KH 801 B 1 HETATM 4 N N3A 2KH . . . J 9 125.823 136.789 148.565 1 26.77 ? N3A 2KH 801 B 1 HETATM 5 O O5' 2KH . . . J 9 126.681 137.587 146.115 1 26.77 ? O5' 2KH 801 B 1 HETATM 6 P PB 2KH . . . J 9 125.267 138.042 149.563 1 26.77 ? PB 2KH 801 B 1 HETATM 7 O O1B 2KH . . . J 9 126.118 139.239 149.438 1 26.77 ? O1B 2KH 801 B 1 HETATM 8 O O2B 2KH . . . J 9 123.875 138.384 149.174 1 26.77 ? O2B 2KH 801 B 1 HETATM 9 O O3B 2KH . . . J 9 125.283 137.526 151.121 1 26.77 ? O3B 2KH 801 B 1 HETATM 10 P PG 2KH . . . J 9 126.703 137.072 151.903 1 26.77 ? PG 2KH 801 B 1 HETATM 11 O O1G 2KH . . . J 9 126.972 135.617 151.637 1 26.77 ? O1G 2KH 801 B 1 HETATM 12 O O2G 2KH . . . J 9 127.859 137.907 151.354 1 26.77 ? O2G 2KH 801 B 1 HETATM 13 O O3G 2KH . . . J 9 126.573 137.298 153.375 1 26.77 ? O3G 2KH 801 B 1 HETATM 14 C C5' 2KH . . . J 9 126.56 139.011 146.043 1 26.77 ? C5' 2KH 801 B 1 HETATM 15 C C4' 2KH . . . J 9 125.496 139.39 145.176 1 26.77 ? C4' 2KH 801 B 1 HETATM 16 O O4' 2KH . . . J 9 125.64 138.74 143.796 1 26.77 ? O4' 2KH 801 B 1 HETATM 17 C C1' 2KH . . . J 9 124.419 138.404 143.42 1 26.77 ? C1' 2KH 801 B 1 HETATM 18 C C2' 2KH . . . J 9 123.433 138.817 144.623 1 26.77 ? C2' 2KH 801 B 1 HETATM 19 O O2' 2KH . . . J 9 122.911 140.165 144.394 1 26.77 ? O2' 2KH 801 B 1 HETATM 20 C C3' 2KH . . . J 9 124.17 138.828 145.699 1 26.77 ? C3' 2KH 801 B 1 HETATM 21 O O3' 2KH . . . J 9 123.578 139.747 146.743 1 26.77 ? O3' 2KH 801 B 1 HETATM 22 N N1 2KH . . . J 9 124.332 136.987 143.16 1 26.77 ? N1 2KH 801 B 1 HETATM 23 C C6 2KH . . . J 9 125.358 136.099 143.634 1 26.77 ? C6 2KH 801 B 1 HETATM 24 C C2 2KH . . . J 9 123.167 136.422 142.393 1 26.77 ? C2 2KH 801 B 1 HETATM 25 O O2 2KH . . . J 9 122.309 137.129 141.993 1 26.77 ? O2 2KH 801 B 1 HETATM 26 N N3 2KH . . . J 9 123.086 134.948 142.137 1 26.77 ? N3 2KH 801 B 1 HETATM 27 C C4 2KH . . . J 9 124.109 134.067 142.612 1 26.77 ? C4 2KH 801 B 1 HETATM 28 O O4 2KH . . . J 9 124.022 132.829 142.383 1 26.77 ? O4 2KH 801 B 1 HETATM 29 C C5 2KH . . . J 9 125.273 134.62 143.375 1 26.77 ? C5 2KH 801 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 72 _model_server_stats.query_time_ms 345 _model_server_stats.encode_time_ms 50 _model_server_stats.element_count 29 #